|
| Status |
Public on Nov 08, 2023 |
| Title |
∆topAPZntopA[pLSROMtopARA] strain, S medium, -NOV, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cell
|
| Organism |
Streptococcus pneumoniae |
| Characteristics |
genotype: deltatopAPZntopA[pLSROMtopARA] from R6
cell type: Bacterial cell
treatment: S medium
|
| Treatment protocol |
Overnight cultures grown in the medium described above were diluted 1000-fold in medium with 0.8% sucrose (noninducing medium) or 0.4% sucrose plus 0.4% maltose (inducing medium) and grown to OD=0.4. To analyze the effect of novobiocin, the antibiotic at 10 x MIC was added to the cultures and they were grown for 30 additional minutes.
|
| Growth protocol |
S. pneumoniae was grown as static cultures at 37ºC in a casein hydrolysate-based liquid medium (AGCH) containing 0.2% yeast extract and 0.8% sucrose (C+Y).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA (about 5 µg) was obtained from samples containing 2-4E8 cells using the RNeasy mini kit (Quiagen). RNA was depleted of ribosomal RNA using the Ribo-Zero (Bacteria) Magnetic Kit (Illumina).
Libraries for RNA-Seq were prepared from 1 µg RNA using the ScriptSeq v2 RNA-Seq system (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Analysis of RNA-Seq data was carried out using the web-based platform Galaxy (European server UseGalaxy.eu).
Quality of raw sequence data from Illumina NovaSeq 6000 was analysed with FastQC tool. Trimming for quality control was conducted with Trimmomatic (Galaxy Version 0.38.1).
Sequencing reads were mapped against the S. pneumoniae R6 genome (ASM704v1) using BWA software package (Galaxy version 0.7.17.4) in simple Illumina mode.
BAM files from BWA were analyzed to obtain the number of reads overlapping each protein-coding gene using program featureCount (Galaxy Version 2.0.1+galaxy2).
Assembly: ASM704v1 RefSeq GCF_000007045.1
Supplementary files format and content: Tab-delimited text files obtained from featureCounts (protein-coding genes), including Reference assembly, Gene ID, Gene name, Start, End and Counts.
|
| |
|
| Submission date |
Sep 13, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Pablo Hernandez |
| E-mail(s) |
[email protected]
|
| Organization name |
Centro de Investigaciones Biologicas (CSIC)
|
| Department |
Cellular and Molecular Biology
|
| Street address |
Ramiro de Maeztu 9
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL28680 |
| Series (1) |
| GSE243041 |
Physiologic and Transcriptomic Effects Triggered by Overexpression of Wild Type and Mutant DNA Topoisomerase I in Streptococcus pneumoniae |
|
| Relations |
| BioSample |
SAMN37378090 |
| SRA |
SRX21765525 |
